Month: September 2015

Genomics England announces interpretation partners and expands industry engagement

Genomics England has today (30th September 2015) announced that it has contracted with Congenica and Omicia to work with them on the interpretation of the genomes from 8,000 patients participating in the 100,000 Genomes Project.  Work with LockheedMartin-Cypher, Nanthealth and WuxiNextcode continues as part of a test phase.  This is in addition to ongoing work with sequencing partner Illumina who are also exploring a variety of bioinformatic challenges around sequencing and clinical interpretation.

Genomics England is also announcing that two new companies, Berg Health and NGM Biopharmaceuticals have joined Genomics England’s industry collaboration, known as the GENE Consortium.  BERG is a Boston based biopharmaceutical company and NGM Biopharmaceuticals is based in South San Francisco.  Both will join the other members of the GENE Consortium who are already working on a year long industry trial assessing how best to engage with Genomics England to accelerate the development of new diagnostics and treatments for patients.

GENE Consortium discussion

GENE Consortium discussion

Sir John Chisholm, Executive Chairman of Genomics England said;

“We are delighted to welcome two new partners to the GENE Consortium.  Exploring how industry will work with this unique dataset along with driving up the quality of the interpretation of genomic data are crucial to us in finding out how to understand and treat disease better in the future.  It’s this that will ensure genomic medicine benefits patients for years to come.”

Garvan partners with Genomics England to advance genomic medicine

The Garvan Institute of Medical Research has signed a memorandum of understanding with Genomics England, the organisation established by the UK’s Department of Health to deliver the world-first 100,000 Genomes Project. The two organisations will share resources and expertise to advance genomic medicine in Australia and the UK.

Mark and John

Professor Mark Caulfield, Genomics England and Professor Marcel Dinger, Kinghorn Centre for Clinical Genomics at Garvan.

The 100,000 Genomes Project will sequence genomes from around 70,000 National Health Service (NHS) patients, focusing on individuals with rare diseases or cancer. Through the project, Genomics England aims to bring benefit to patients, build capability in the burgeoning area of genomic medicine, and advance medical research.

Under the terms of the agreement, Garvan and Genomics England will work together to make genomic information more accessible, meaningful and usable, particularly by developing better ways to capture clinical information and integrate it with genomic data.

In addition, the two institutions will collaborate to develop next-generation genomics databases and to establish clear ethical and legal frameworks around the use of genomic information. They will also collaborate to design educational resources about clinical genomics for health professionals and the wider public.

Professor John Mattick, Executive Director of Garvan, says that partnering with Genomics England is an important step in the development of Australia’s genomics capacity.

Professor Mattick says, “This agreement is an important step for both nations. It enables us to use our complementary expertise to advance our shared vision of the global transformation of medicine through the use of genomic information.”

Garvan logoProfessor Mark Caulfield, Chief Scientist at Genomics England, says, “I am delighted we are collaborating with the Garvan Institute of Medical Research in Australia. This partnership will allow us to share tools and approaches to harmonise datasets in Australia and the UK. Our aim is to support other countries in establishing similar programmes to the 100,000 Genomes Project around the world.”

As one of Australia’s leading medical research institutions, Garvan develops research programs that combine leading-edge science with clinical outcomes. In 2012, Garvan established the Kinghorn Centre for Clinical Genomics (KCCG), the largest sequencing centre in the southern hemisphere. KCCG is undertaking research and developing innovative analytical pipelines to advance the use of whole-genome sequencing in clinical diagnosis and patient care.

New rare disease gene tool launched – PanelApp

PanelAppGenomics England has developed a unique resource, the ‘PanelApp’. It is a new crowdsourcing tool for the scientific community, allowing knowledge of rare disease genetics to be shared and evaluated. This will create comprehensive evidence-based gene panels for rare diseases. The resource is publically available for anyone who would like to view and download the gene panels. Experts can register as a reviewer to make evaluations of the gene panels.

 We are encouraging those with an expertise in rare disease genetics to register to be a reviewer. We’d like experts to help finalise the list of genes that can be used to help diagnose a rare disease

Dr Ellen McDonagh, Lead Scientific Curator at Genomics England said: “We’ve developed the PanelApp to crowd source knowledge of genetic testing for rare diseases and provide a tool for experts to utilise. We are encouraging those with an expertise in rare disease genetics to register to be a reviewer. We’d like experts to help finalise the list of genes that can be used to help diagnose a rare disease. The PanelApp also allows evidence for research grade genes to be collected, which may eventually be promoted to clinical grade as more evidence emerges. Currently gene panels differ from place to place; PanelApp is an opportunity to encourage standardisation of gene panels throughout the scientific community, based on expert knowledge and guidelines.”

The 100,000 Genomes Project is recruiting patients with 122 different rare diseases. For these patients the underlying genetic cause of their rare disease is not known, or is not certain. By looking at a person’s genome it is hoped that the likely genetic change that is causing their rare disease will be identified, and that they will be provided a diagnosis for the first time. In some cases this will help guide treatment to slow or halt progression of the disease.

There are millions of genetic variations between people. To help identify the genetic change that may be causing a rare disease, genome analysts use a variety of tools and techniques to narrow their search. One of these tools is a list of genes known to be involved in the rare disease. This separates the genetic changes in these genes from the rest of the genome, as they may be more likely to cause the disease.

For each rare disease that is a part of the 100,000 Genomes Project, a list of potential genes for each condition has been gathered – a gene panel. Four publicly available resources were used to create the panels. The role of some genes is understood and the effects they have on cells and the body has been discovered. Some of these genes are already tested for by the NHS to diagnose disease. For other genes, their function is less clear. Expert reviewers are being asked to assess the panels and provide evidence that a specific gene is involved in the disease.

Reviewers are asked to give each gene a rating on a scale of green = high evidence i.e. the gene is very likely be the cause of the disease and can be reported back to patients, to red = low evidence for a role in disease, or not suitable for clinical diagnosis at this time. Their ratings can be based on clinical or research-acquired knowledge. Reviews will then be consolidated based upon criteria established by Genomics England. Experts can also add new genes to the panel, and it is expected that the gene panels will be updated as we learn from the 100,000 Genomes Project data.

The wider clinical and scientific community are able to access and review the panels, and over time this will improve understanding of diseases.

Visit the PanelApp, or view the videos for a guide and demonstration.

Genomics at NHS Expo 2015

The 100,000 Genomes Project had an exhibition stand at the UK’s major health and care conference, NHS Expo. The stand brought together key partners working on this ground-breaking project: Genomics England, Department of Health, NHS England and Health Education England. We also shared the stand with illumina, Congenica and WuXi NextCODE – innovative companies providing genome sequencing and genome interpretation for the Project.

Delegates came to visit our shared exhibition stand to learn more about genomics, including how DNA is sequenced, what happens with the results, and how these are interpreted.

Secretary of State for Health Jeremy Hunt visiting the stand

Secretary of State for Health Jeremy Hunt visiting the stand

Attendees could extract their own DNA with help from colleagues from Manchester NHS Genomic Medicine Centre. Visitors can also follow the entire ‘journey’ each participant in the Project makes – from giving their consent to take part, to having their whole genome sequenced and the crucial annotation and interpretation of that data which leads to the feedback they eventually receive from their clinician.

We welcomed several VIPs to the stand. Secretary of State for Health Jeremy Hunt, Minister for Life Sciences George Freeman, Sir Malcolm Grant, Chair of NHS England, and Dame Una O’Brien, Permanent Secretary at the Department of Health were among the visitors.

DNA Extraction Demo

DNA Extraction Demo

Professor Bill Newman, who is leading on the 100,000 Genomes Project at the Manchester Centre for Genomic Medicine (MCGM) said: “Saint Mary’s Hospital and The University of Manchester are delighted, in collaboration with other colleagues in Greater Manchester, to play a leading part in the 100,000 Genomes Project and the opportunity it presents to bring the latest genomic medicine to patients in our area.”

“Our stand at NHS Expo is just one part of our strategy developed by the Public Programmes Team at Central Manchester University Hospitals to engage the public with genomic science, and will show how we do that. People will be able to extract their own DNA from their cells – a fascinating process. ”

Check out our Storify for a roundup of tweets from the event.